Hi Lea,

Thanks for the tips!

I think I did something similar for a previous test without hipo segmentation (took nearly 3 to 4h).
I will check the way I've got to set the number of cpu per tasks, just in case.

Thanks

Alex

Message: 20
Date: Fri, 20 Apr 2018 09:19:12 +0000
From: "Backhausen, Lea" <Lea.Backhausen@uniklinikum-dresden.de>
Subject: Re: [Freesurfer] SLURM - speed processing (Alexandre Obert)
To: "'freesurfer@nmr.mgh.harvard.edu'"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1D0E7A9ED60D3E4399550C3A60C0BADC394606B6@G06EDBN1.med.tu-dresden.de>
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External Email - Use Caution

Hi Alex,

I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on how to parallelize it, how much ressources to ask for? This is what I learned:

1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess for the commands mri_em_register, mri_ca_register and mri_ca label used in the steps Skull Stripping, EM registration, CA reg and Subcortical registration).
2) From Version 6.0.0 FreeSurfer is also able to process the two hemispheres in parallel instead of sequentially (steps 16 ? 30).

Taking advantage of these changes reduces processing time dramatically. If I use 4 CPU per task on SLURM instead of 1 the processing time drops form around 8 hours to around 4 or 4 ? hours. Increasing the CPU per task did not improve processing time much though, so to save a bit CPU time now use 4 CPU regularly.
I don?t know if you have to submit your jobs exactly the same way but a typical job file for me looks like this:

------------------------------------------------------------------------------------
#!/bin/bash
#SBATCH --time=10:00:00
#SBATCH --output=/your_working_directory/job-%j.out
#SBATCH --error=/your_working_directory/job-%j.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --partition=haswell
#SBATCH --mem-per-cpu=2500
#SBATCH -A your_project_name

module load modenv/eb
module load FreeSurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

export SUBJECTS_DIR=/your_subjects_directory

recon-all -s your_subject_ID -all -parallel -openmp 4
--------------------------------------------------------------------------------------

Of course you can just add the ?hippocampal-subfields-T1 tag flag your command.
I found that asking for 2500 MB works just fine for 4CPU per task (as the 2500 is multiplied times 4 in this case). The maximum RAM was about 7000 KB for my jobs.
Just make sure you add the? -parallel -openmp 4? flag to your command line AND ?#SBATCH --cpus-per-task=4? to your job file, otherwise the parallelization will not work.

Hope this helps! Get back to me if you have any more questions!

Best,
Lea

------------------------------
Lea Backhausen
Research Assistant

Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany
http://www.uniklinikum-dresden.de

------------------------------

Message: 5
Date: Thu, 19 Apr 2018 17:05:46 +0200
From: Alexandre Obert <obert.alexandre@gmail.com>
Subject: [Freesurfer] SLURM - speed processing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAGTEUh_XypWu4h+4ban62BfH8idf96HEquUL+OMMaWT_GEk4Cw@mail.gmail.com>
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Hi all,

I'm definitively a noob with both freesurfer and SLURM processes and I wonder if anyone could give me some advice.
I tried processing a subject (including hippocampal segmentation) using the following command (freesurfer 6.0.0):

recon-all -all -s s03 -hippocampal-subfields-T1

It took nearly 12h to process.
I then submit this job to a supercomputer (using slurm) and I asked for nearly 30Go RAM It took nearly 7h to process. That seems good but I wonder if it's possible to speed it up a little more?

Regards,

Alex
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Message: 6
Date: Thu, 19 Apr 2018 11:57:45 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI for the lobar annotation
To: "Fernanda Hansen P. de Moraes" <fernandahmoraes@gmail.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9822cb24-192a-2713-0418-b215da87d27e@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

yes

On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote:
> Douglas, thank you very much again.
> So I can assume it is the lGI for the area (in this case the lobe)?
>
> Thank you again!
>
> On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve <dgreve@mgh.harvard.edu
> <mailto:dgreve@mgh.harvard.edu>> wrote:
>
> The "intensity" is the mean value of the input (lh.pial_lgi in
> this case) averaged over vertices. If? you wan the total number,
> multiply it by the number of vertices or re-run with --accumulate.
> The area is the surface area of the entire lobe.
>
>
> On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote:
>> Sorry, my mistake.
>>
>> mri_segstats --annot DA011 lh lobesStrict --i
>> DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats
>>
>> On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve
>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>
>> What is your command line? Also, please remember to post to
>> the list
>>
>>
>> On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote:
>> > Dear Douglas,
>> >
>> > thank you.
>> >
>> > ?The code worked, but I didn't understand the result very
>> well. What
>> > means intensity? The area, is the ara from the piall_lgi
>> surface
>> > (outer surface)?
>> >
>> > Thank you again
>> >
>> > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve
>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>
>> > <mailto:dgreve@mgh.harvard.edu
>> <mailto:dgreve@mgh.harvard.edu>>> wrote:
>> >
>> >? ? ?If you run it with --help you will see an example
>> >
>> >
>> >? ? ?On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote:
>> >>? ? ?Thank you, Douglas,
>> >>
>> >>? ? ?do you have any suggestions?on how to make you work?
>> >>
>> >>? ? ?Fernanda
>> >>
>> >>
>> >>
>> >>? ? ?On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve
>> >>? ? ?<dgreve@mgh.harvard.edu
>> <mailto:dgreve@mgh.harvard.edu>
>> <mailto:dgreve@mgh.harvard.edu
>> <mailto:dgreve@mgh.harvard.edu>>> wrote:
>> >>
>> >>? ? ? ? ?that should work, except the command line is not
>> quite right
>> >>
>> >>
>> >>? ? ? ? ?On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes
>> wrote:
>> >>>? ? ? ? ?Good night,
>> >>>
>> >>>? ? ? ? ?does anyone know if it is possible to calculate
>> the lGI for
>> >>>? ? ? ? ?the ?h.lobesStrict.annot? And if it yes, how can
>> I do it?
>> >>>
>> >>>? ? ? ? ?I've already tried to use:
>> >>>
>> >>>? ? ? ? ?/mri_segstats --annot
>> subjxx/label/lh.lobesStrict.annot --i
>> >>> ?$SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum
>> >>> ?lh.lobesStrict.annot.pial_lgi.stats/
>> >>>
>> >>>? ? ? ? ?Thank you!
>> >>>? ? ? ? ?--
>> >>>? ? ? ? ?Fernanda Hansen P. de Moraes
>> >>>? ? ? ? ?F?sica M?dica | Instituto D'Or de Pesquisa e
>> Ensino?| Rede
>> >>>? ? ? ? ?D'Or S?o Luiz
>> >>>
>> >>>
>> >>> ?_______________________________________________
>> >>>? ? ? ? ?Freesurfer mailing list
>> >>> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >>>? ? ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >> ?_______________________________________________
>> >>? ? ? ? ?Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >>? ? ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >>? ? ? ? ?The information in this e-mail is intended only
>> for the
>> >>? ? ? ? ?person to whom it is
>> >>? ? ? ? ?addressed. If you believe this e-mail was sent to
>> you in
>> >>? ? ? ? ?error and the e-mail
>> >>? ? ? ? ?contains patient information, please contact the
>> Partners
>> >>? ? ? ? ?Compliance HelpLine at
>> >> http://www.partners.org/complianceline . If the e-mail was
>> >>? ? ? ? ?sent to you in error
>> >>? ? ? ? ?but does not contain patient information, please
>> contact the
>> >>? ? ? ? ?sender and properly
>> >>? ? ? ? ?dispose of the e-mail.
>> >>
>> >>? ? ?--
>> >>? ? ?Fernanda Hansen P. de Moraes
>> >>? ? ?F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?|
>> Rede D'Or
>> >>? ? ?S?o Luiz
>> >>
>> >>
>> >> ?_______________________________________________
>> >>? ? ?Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Fernanda Hansen P. de Moraes
>> > F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede
>> D'Or S?o Luiz
>>
>> --
>> Fernanda Hansen P. de Moraes
>> F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede D'Or
>> S?o Luiz
>
> --
> Fernanda Hansen P. de Moraes
> F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede D'Or S?o
> Luiz

------------------------------

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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

End of Freesurfer Digest, Vol 170, Issue 31
*******************************************

------------------------------

Message: 21
Date: Fri, 20 Apr 2018 11:19:27 +0100
From: "C.P.E. Rollins" <cper2@cam.ac.uk>
Subject: Re: [Freesurfer] FSGD design for multi-centre study
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <b262bd397c7854132bad39678373b1c3@cam.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed

External Email - Use Caution

Thanks a lot for the explanation. The issue is that I don't think
Freesurfer will run a design for which there are no subjects for a given
class. So if I keep the classes (24 classes since 6 centres x 2 gender x
2 groups (patient vs. control), and have the contrast with 12 (-1) and
12 (1),
-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0
I get the error:
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
--------------------------------
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

I'm assuming this is because there are no participants in, for example,
patient_centre2_female
Is there any way to get around this issue, or should I remove those
centres from my analysis (since I can't only remove
"patient_centre2_female", as this would make the contrast unbalanced
(positives and negatives would not add to the same number). I hope this
was clear but please let me know if it was not.

Thanks again,
Colleen

------------------------------

Message: 22
Date: Fri, 20 Apr 2018 12:20:10 +0200
From: Daniel Margulies <daniel.margulies@gmail.com>
Subject: [Freesurfer] 8th Annual Brain-Art Competition @ OHBM open for
submissions!
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAA9bqVrA9+TO3pmKrVYOXRYM2nuECZP=2syDwqccKjwmBsvDFg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

In order to recognize the beauty and creativity of artistic renderings
emerging from the neuroimaging community, we are launching the eighth
annual Brain-Art Competition.

Countless hours are devoted to the creation of informative visualizations
for communicating neuroscientific findings. The Brain-Art Competition aims
to recognize this often unappreciated aspect of the publication process,
and highlight the artistic creativity of our community.

We are inviting researchers to submit their favorite unpublished works for
entry. Both team and single-person entries are welcomed. The competition
will have six award categories:

1. Best Representation of the Human Connectome
2. Best Abstract Brain Illustration
3. Best Humorous Brain Illustration
4. Best Video Illustration of the Brain
5. Updating classics
6. Special Topic: Comparative neuroanatomy

The last two categories are new additions for the 2018 competition:

"Updating classics" invites submissions that bring fresh ideas, data, and
visualization techniques to famous illustrations from the neuroscience
canon.

With the increasing availability of non-human brain data, the special topic
in "comparative neuroanatomy" invites submissions that address the
visualization challenge of translating findings across species. How can
cross-species information be more effectively be presented?

Submission Deadline: 11:59PM CDT, Wednesday, June 6th, 2018

Award Notification: Monday, June 18th, 2018

For more information, check out the competition details:
http://www.neurobureau.org/brainart/
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Message: 23
Date: Fri, 20 Apr 2018 12:13:11 +0000
From: "Boggess, Matthew Jozsef" <MBOGGESS@mgh.harvard.edu>
Subject: Re: [Freesurfer] fmriprep to fsfast interface
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CY1PR04MB19274A32BF93228DEDE20EF993B70@CY1PR04MB1927.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Thank you for the response!

I'm interested primarily in tal space, but potentially native as well. For tal space, is there no easy way to just directly transform the data into tal space or provide an identity matrix for the registration?

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, April 17, 2018 12:01:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fmriprep to fsfast interface

sorry for the delay, see below

On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote:

Hello,

I just wanted to follow up to see if anyone could help with any of my questions, particularly # 1.

Thank you!

Matt Boggess

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Boggess, Matthew Jozsef <MBOGGESS@mgh.harvard.edu><mailto:MBOGGESS@mgh.harvard.edu>
Sent: Thursday, April 5, 2018 8:02:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] fmriprep to fsfast interface

Hello,

I've been working on taking the outputs of the fmriprep BOLD preprocessing tool (https://fmriprep.readthedocs.io/en/latest/index.html) and coercing them into the fsfast structure so that first levels can be run with mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than anticipated and I was hoping to get some help verifying my current approach (attached to this email).

Question 1:

fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 is not an option). However, the typical spatial normalization workflow uses a registration matrix from the bold to T1 to transform to talairach. Is there a way to do this transformation without having to specify a registration matrix given the functional data is already in the T1 space? My current approach is to use mri_convert with the --apply_transform flag pointing to the talairach.xfm registration matrix in the subject's recon folder, but I am not sure if this is a reasonable workaround.
Do you want to analyze it in the native T1 space or in talairach space? If native, then when you run mkanalysis-sess you can bypass the preprocessing by directly specifying the stem of the functional data you want to process (-funcstem). If tal space, then I think it should work out of the box (it would recalc the registration, but that should be ok).

Question 2:

fsfast normally calculates the global mean value of the raw data to be used for intensity normalization. However, with fmriprep I only have access to the preprocessed data in T1 space. Would extracting the global mean value for intensity normalization from the preprocessed BOLD in T1 space be valid?
Yes

Question 3:

Is there a way to do first levels in the native subcortical space? If so, what is the filename structure expected (maybe mni305.2mm gets replaced with the subject name as with the surface data)? I've only seen examples transforming to mni305 space, but ideally an option would be to just transfer the preprocessed BOLD in T1 space and run first levels staying in the native T1 space.
See above.

Thanks for your help!

Matt

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------------------------------

Message: 24
Date: Fri, 20 Apr 2018 15:15:06 +0300
From: Zohar Berman <zorkush@gmail.com>
Subject: Re: [Freesurfer] Calculation of surface area
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAOu_4t3Do224twg+CtmWns0SS4USEESjPU2Lvhi6jr-dBO33DA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Dear Douglas,

Thank you for your quick answer!
The thing is, we don't have access to the original surface area files which
were created by FreeSurfer anymore. Thus, we were wondering if we can
calculate a region's surface area if we have its volume & cortical
thickness values.
Is that possible?

Thank you very much!
Zoi

On 20 April 2018 at 00:04, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

> We output surface area separately both as a map and as statistics
>
>
> On 04/19/2018 04:47 PM, Zohar Berman wrote:
> > Dear FreeSurfer experts,
> >
> > Can one use the volume and cortical thickness of a region to calculate
> > the surface area of this region?
> >
> > Thanks a lot in advance!
> > Best,
> > Zoi
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Message: 25
Date: Fri, 20 Apr 2018 12:46:17 +0000
From: "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Subject: Re: [Freesurfer] using T2 for hippo subfields
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CY1PR0201MB1914CD281130FCBAA1ECE228D6B40@CY1PR0201MB1914.namprd02.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

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Ok. Can you run -hippocampal-subfields-T1 without the -hires flag using a submillimeter T1?

Jim
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
Sent: Friday, April 20, 2018 2:24:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution

Sorry, I?m not sure I follow. But, if you run recon-all with the hires flag, then you can just run ?hippo-subfields-T1 and it?ll take advantage of the high resolution.

--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 20 April 2018 at 01:34
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution

Yes the output appears ok.
I was under the impression there would be benefits from using the -hires flag with submillimeter T1s as input.

If you suggest not having to use the -hires flag in our case (because of little benefit from 0.8mm input compared to 1mm), I presume I can still use the -hippocampal-subfields-T1 option in the traditional recon-all -all stream?

Jim

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
Sent: Thursday, April 19, 2018 1:57:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution

Hi Jim,
>From my experience .8 isotropic is on the edge. Did you take a look at the output? You can always send us the data if you want us to take a look.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 19/04/2018, 19:55, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dimitriosalexopoulos@wustl.edu> wrote:

External Email - Use Caution

Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm through the standard recon-all -all stream, with the -hires flag (but with no experts file). The volumes and surafces look good. Is there any need to be concerened with the output since I did not use an experts file?

Jim

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, April 04, 2018 7:52 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] using T2 for hippo subfields

no it is not required

cheers
Bruce
On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote:

> Per an earlier post below, is an 'expert_file' always required when using the -hires option?
>
> Jim
>
> ______________________________________________________________________
> ______________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos,
> Dimitrios <dimitriosalexopoulos@wustl.edu>
> Sent: Sunday, March 25, 2018 9:47:07 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm
> isotropic) using the -hires flag, with no expert file, which generated nice surfaces.
>
> Is an 'expert_file' required ??
>
>
> Jim
>
> ______________________________________________________________________
> ______________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias
> Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
> Sent: Friday, March 23, 2018 11:02:00 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Hi Jim,
>
> In the end it's an empirical question, but my gut feeling is that the
> T1 with hi-res flag will be best.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios"
> <dimitriosalexopoulos@wustl.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Friday, 23 March 2018 at 16:00
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] using T2 for hippo subfields
>
>
>
> Hi. We are acquiring sequences on a pediatric cohort that include a
> T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd
> like to run the hippocampal subfields module on the subjects using FS 6.0.
>
>
>
> Is it recommended/useful to run the multispectral segmentation mode
> with the additional lower resolution T2 sequence?
>
> I read that you really only benefit if the T2 is of similar or better resolution than the T1.
>
>
>
> If that's the case, would it be best to just run with the single T1
> but with the hi-res flag in the recon-all command?
>
>
> Thanks.
>
> Jim
>
>
>
>
>
>
>
>
>
>
>
>
> ______________________________________________________________________
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>
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End of Freesurfer Digest, Vol 170, Issue 33
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